qiime 2.0.6: data provenance, simplified viewing, and new forum

We're excited to announce the 2.0.6 minor release of the QIIME 2 framework and supporting plugins. This is the second synchronized release, meaning that we intend all interfaces and plugins versioned 0.0.6 to work with QIIME 2.0.6. For information about QIIME 2, see https://qiime2.org.

The 2.0.6 synchronized release includes the following new features and interface changes. We aren’t listing all changes here, just the ones we are most excited about and those that will affect end users. For future releases, as the QIIME 2 project is now beginning to stabilize, we are committed to documenting all user-facing changes in changelogs instead of the summary below.

New features:

• New .qza/.qzv file format supporting decentralized data provenance tracking. Provenance can be visualized and inspected by uploading a .qza/.qzv file to https://view.qiime2.org (more details about this service below). Other provenance visualization/inspection will be available in the future. Note: data generated with QIIME 2.0.5 will continue to be supported in the current and future releases, though the data will not contain provenance information. All new data generated with QIIME 2.0.6 will contain provenance information.
• https://view.qiime2.org is a new service for viewing .qza/.qzv files in the browser without requiring QIIME 2 to be installed. This service is great for sharing QIIME data with collaborators who may not have QIIME 2 installed. In addition to file uploads, the service supports viewing .qza/.qzv files accessible via URLs (e.g. Dropbox, Google Drive, GitHub links).
• https://docs.qiime2.org is the new site for accessing QIIME 2 user documentation. Many improvements have been made to the site, including links to all data files generated in tutorials and other documentation. These precomputed .qza/.qzv files can be easily viewed at https://view.qiime2.org or downloaded directly. By providing precomputed results, it is possible to read the tutorials and view results without installing QIIME 2 or additional software.
• New QIIME 2 forum (separate from the QIIME 1 forum) for user and developer support, community discussion, announcements, etc: https://forum.qiime2.org
• Support for exporting data from .qza/.qzv files (new CLI command qiime tools export and API qiime.sdk.Result.export_data).
• qiime taxa barplot has more discrete color palettes and can remove sorting categories, among several other bug fixes and usability enhancements.
• Most visualizations have been updated to have a consistent look-and-feel, and many have improved usability and functionality.

Interface changes:

• Removed HELP_URL, CITATION, and CONDA_CHANNEL from qiime.sdk API.
• qiime feature-table filter has been removed in place of qiime feature-table filter-samples and filter-features, which provide many more table filtering operations. The previous filtering functionality provided by qiime feature-table filter is now available in qiime phylogeny filter-table.
• qiime feature-table view-seq-data is now qiime feature-table tabulate-seqs.
• qiime feature-table view-taxa-data is now qiime taxa tabulate.
• qiime diversity core-metrics --p-counts-per-sample is now --p-sampling-depth.

We're very grateful to all of the plugin developers who have contributed functionality to this pipeline.

Because our microbiome analysis functionality is still currently very new, QIIME 2 is not yet recommended as a replacement for QIIME 1, but we are very interested in having users test QIIME 2 and give us feedback.

In addition to user testing, we're also interested in working with developers to contribute new QIIME 2 plugins or interfaces. You should read our draft plugin developer documentation at https://qiime2.org to get started. While QIIME 2 is in its alpha release stage, backward incompatible interface changes that impact plugins and interfaces can and will occur.

As always, thanks for your interest in QIIME!